Reference SNP(refSNP) Cluster Report: rs9476886

Reference SNP(refSNP) Cluster Report: rs9476886

refSNP ID: rs9476886
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3
Citation:	PubMed

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_032122.3:c.56+1584G>A
NM_183040.1:c.56+1584G>A
NM_183041.1:c.-233+1584G>A
NT_007592.14:g.6519712C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss17877534 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9476886 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss13110104	SC_SNP\|NT_007592.13_6519712	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	10/22/03	10/31/03	119	Genomic	unknown
ss17877534	CSHL-HAPMAP\|CSHL-HuCC-200402.chr6.NT_007592.13_6519712	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	02/19/04	10/26/06	120	Genomic	unknown
ss44721136	ABI\|hCV3114521	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	07/19/05	07/19/05	126	Genomic	unknown
ss68966329	PERLEGEN\|PGP13295890	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	01/30/07	03/31/08	127	Genomic	unknown
ss75162583	ILLUMINA\|ILMN_Human_1M_rs9476886	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	08/28/07	08/29/07	129	Genomic	unknown
ss80779118	KRIBB_YJKIM\|KHS1016297	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	11/26/07	11/26/07	130	Genomic	unknown
ss85474002	HGSV\|Cor19129_SNV_20070510.chr6_15769440	fwd/B	C/T	aaaacgaggctgggcgcagtgactaatacc	ataatcccaccacttcaggaagcctaggag	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 GCAAGCACAC CCATCAGTGA ATGACTCCGA GCGTCCATAA CTTTCTAAAC ACCAAACTAA
 CAAAAATGAT TGACGCATGG TAAGTGCTCA AGCGTTTGAC AGTTTGTTAT TCAACGCCCA
 ATGTGCAAAT AGTATTAACA TTTTTGTCCA TTAAGATAAA ATTTTGGCTA ACATCTTTCT
 CATTAGAAAT TTAAAACGAG gctgggcgca gtgactaata cc
 Y
 ataatcccac cacttcagga agcctaggag ggaggatctc ttgtacccag gagttggagg
 ctgcagcgag ctataatagc gccactgcgc tccagcctgg gcaacagagc gagaacttgt
 cactttaaaa aaaaGGGGGG GAGGGTGggc cgggaacggt ggcacacgcc tgtaatccca
 gcactttggg aggccaaggc gggaggatca caaggtcagg agttcgagac cagcctggcc
 aatatggtga aacccgtctc tactaaaaaa tacaaaaata agccgggcgc ctctagtccc
 agctactcag gaggtggagc caggagaatc gcttgaatcc gggaggcggc ggttgcagtg
 agccgagatc acgccactgc actccagtct gggtgacaga gcaagactcc atctcaaaaa
 aaaGGGGGGT GGGGGGGAGA AATTTAAAAC AGTATGAGTG GAAATGTTCT CACATTCAGT
 GCATCCTCCA ACAGGATTTG

GeneView

GeneView via analysis of contig annotation: DTNBP1 dystrobrevin binding protein 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_007592->NM_032122

function

reference

NT_007592->NM_183040

function

reference

NT_007592->NM_183041

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_007592->NM_032122->NP_115498	6519712	reverse	intron

reference	NT_007592->NM_183040->NP_898861	6519712	reverse	intron

reference	NT_007592->NM_183041->NP_898862	6519712	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9476886 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838973.1	11953180	15608143	plus	C	alt_assembly_8	HuRef	HuRef	view	222
6	NT_007592.14	6519712	15769440	plus	C	ref_assembly	reference	reference	view	222
6	NW_922984.1	15294672	16899416	plus	C	alt_assembly_1	Celera	Celera	view	222

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592

dbSNP Blast Analysis
GenBank HTGS Finished:
AL022343.6

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss17877534	HapMap-CEU	European	120	IG	0.550	0.400	0.050	0.655	0.750	0.250

	HapMap-HCB	Asian	90	IG	0.378	0.556	0.067	0.150	0.656	0.344

	HapMap-JPT	Asian	86	IG	0.372	0.419	0.209	0.371	0.581	0.419

	HapMap-YRI	Sub-Saharan African	116	IG	0.241	0.569	0.190	0.294	0.526	0.474

ss68966329	HapMap-CEU	European	120	GF	0.550	0.417	0.033		0.758	0.242

	HapMap-HCB	Asian	90	GF	0.356	0.600	0.044		0.656	0.344

	HapMap-JPT	Asian	90	GF	0.311	0.578	0.111		0.600	0.400

	HapMap-YRI	Sub-Saharan African	118	GF	0.237	0.576	0.186		0.525	0.475

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss17877534	247	91	125	27
ss68966329	247	93	126	27

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs9476886	270	93	127	27

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
157	ss17877534	C/C	CSHL-HAPMAP	HapMap-CEU	NA12144	CEPH1334.10	r23_ch6_CEU_illumina:golden_gate_1.0.0	504535
157	ss68966329	C/T	CSHL-HAPMAP	HapMap-CEU	NA12144	CEPH1334.10	chr6-HapMap-CEU
159	ss17877534	T/T	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	r23_ch6_CEU_illumina:golden_gate_1.0.0	504535
159	ss68966329	C/T	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	chr6-HapMap-CEU
252	ss17877534	C/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r23_ch6_CEU_illumina:golden_gate_1.0.0	504535
252	ss68966329	C/C	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	chr6-HapMap-CEU
254	ss17877534	C/T	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	r23_ch6_CEU_illumina:golden_gate_1.0.0	504535
254	ss68966329	C/C	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	chr6-HapMap-CEU
465	ss17877534	C/T	CSHL-HAPMAP	HapMap-CEU	NA12004	CEPH1420.10	r23_ch6_CEU_illumina:golden_gate_1.0.0	504535
465	ss68966329	C/C	CSHL-HAPMAP	HapMap-CEU	NA12004	CEPH1420.10	chr6-HapMap-CEU
466	ss17877534	C/C	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	r23_ch6_CEU_illumina:golden_gate_1.0.0	504535
466	ss68966329	C/T	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	chr6-HapMap-CEU
5141	ss17877534	C/C	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	r23_ch6_YRI_illumina:golden_gate_1.0.0	504535
5141	ss68966329	C/T	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	chr6-HapMap-YRI
5150	ss17877534	C/C	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r23_ch6_HCB_illumina:golden_gate_1.0.0	504535
5150	ss68966329	C/T	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	chr6-HapMap-HCB
5151	ss17877534	C/T	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r23_ch6_HCB_illumina:golden_gate_1.0.0	504535
5151	ss68966329	C/C	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	chr6-HapMap-HCB
5165	ss17877534	C/C	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r23_ch6_HCB_illumina:golden_gate_1.0.0	504535
5165	ss68966329	C/T	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	chr6-HapMap-HCB
5171	ss17877534	C/C	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	r23_ch6_HCB_illumina:golden_gate_1.0.0	504535
5171	ss68966329	C/T	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	chr6-HapMap-HCB
5178	ss17877534	C/T	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	r23_ch6_HCB_illumina:golden_gate_1.0.0	504535
5178	ss68966329	C/C	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	chr6-HapMap-HCB
5190	ss17877534	T/T	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	r23_ch6_HCB_illumina:golden_gate_1.0.0	504535
5190	ss68966329	C/T	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	chr6-HapMap-HCB
5201	ss17877534	T/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5201	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	chr6-HapMap-JPT
5211	ss17877534	T/T	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5211	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	chr6-HapMap-JPT
5220	ss17877534	C/C	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5220	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	chr6-HapMap-JPT
5223	ss17877534	T/T	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5223	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	chr6-HapMap-JPT
5224	ss17877534	C/C	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5224	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	chr6-HapMap-JPT
5226	ss17877534	C/C	CSHL-HAPMAP	HapMap-JPT	NA18990	JA18990	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5226	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18990	JA18990	chr6-HapMap-JPT
5234	ss17877534	T/T	CSHL-HAPMAP	HapMap-JPT	NA18999	JA18999	r23_ch6_JPT_illumina:golden_gate_1.0.0	504535
5234	ss68966329	C/T	CSHL-HAPMAP	HapMap-JPT	NA18999	JA18999	chr6-HapMap-JPT
5253	ss17877534	C/C	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r23_ch6_YRI_illumina:golden_gate_1.0.0	504535
5253	ss68966329	C/T	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr6-HapMap-YRI
5260	ss17877534	C/T	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r23_ch6_YRI_illumina:golden_gate_1.0.0	504535
5260	ss68966329	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	chr6-HapMap-YRI
5297	ss17877534	C/C	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	r23_ch6_YRI_illumina:golden_gate_1.0.0	504535
5297	ss68966329	C/T	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	chr6-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .